Discovery of Fragment Length of Circulating Tumor DNA Might Increase Liquid Biopsy Sensitivity
The liquid biopsy may be a welcome reprieve from typical biopsies. The minimally invasive test could reduce the need for the sometimes painful and risky procedures involved in sampling tumors, particularly those that reside deep within the body. However, thus far, the utility of the test has been limited by its sensitivity, particularly in its detection of solid tumors that have not yet metastasized.
A study led by the University of Utah School of Medicine reported an advance that could directly increase the sensitivity of liquid biopsies. Liquid biopsies detect pieces of DNA from tumors that are shed into the blood. But circulating tumor DNA can be difficult to pick out from the abundant pieces of circulating DNA from healthy cells. Published by Underhill et al in PLOS Genetics, the study demonstrated that the fragments of circulating tumor and healthy DNA in cancer patients were differently sized, a property that can be exploited to distinguish between the two types of DNA.
“This development has the potential to enable earlier detection of solid tumors through a simple blood draw by substantially improving our ability to detect very low quantities of circulating DNA derived from tumor cells,” said corresponding author Hunter Underhill, MD, PhD, who initiated the research while in the laboratory of senior author Jay Shendure, MD, PhD, Professor in Genome Sciences at the University of Washington.
Discovery in Animal Models
The size difference between tumor and healthy circulating DNA was initially discovered in animal tumor models created by inducing tumors with human cancer cells. In a model of glioblastoma, a brain cancer that does not tend to metastasize outside of the brain, researchers could readily see the length of circulating tumor DNA was smaller than healthy DNA by 20 to 50 base pairs. This size difference was then confirmed in an animal model of liver cancer, indicating the size difference may be present in more than one type of tumor. However, it was unclear at this stage in their research whether this was a species-specific finding limited to animal tumor models or a biologic phenomenon that may also be present in cancer patients.
Further Investigation
The investigators then compared circulating DNA from melanoma patients with that from healthy volunteers. They found that their observations from animal models held true in that the average length of all the DNA pieces present in the blood was 20 to 50 base pairs shorter than the DNA pieces in blood from healthy volunteers. Upon sequencing the DNA, they found that DNA fragments containing mutated genes were typically smaller than healthy versions of the gene from the same patient.
The results suggested that circulating tumor DNA is more likely to be shorter than circulating healthy DNA. Therefore, Dr. Underhill explained, selecting for pieces that are smaller should enrich for DNA that comes from tumors. If a person carries them, separation of specific DNA fragments based on size should make them easier to see.
To test the notion, scientists examined DNA from four patients with lung cancer, isolating fragments that were 20 to 50 base pairs shorter than the total average size in circulation. Doing so increased the proportion of tumor to healthy DNA by 2.5- to 9-fold. The approach was successful in making a difference in samples from the two patients in whom the smaller-sized tumor DNA was not readily apparent, which may represent patients with low tumor burden and previously difficult-to-detect circulating tumor DNA.
“It's possible that jump in sensitivity could make the difference between being able to detect a cancer and not,” said Dr. Underhill. Together, the findings support the idea that sorting for smaller DNA fragment size could increase the sensitivity of liquid biopsies for tracking many different types of cancers.
Dr. Underhill also pointed out the discovery may reveal there is something fundamentally different about how the body processes tumor DNA in circulation.
The content in this post has not been reviewed by the American Society of Clinical Oncology, Inc. (ASCO®) and does not necessarily reflect the ideas and opinions of ASCO®.
